Changeset 221

Timestamp:

Dec 20, 2006, 3:07:20 PM (16 years ago)

Author:

Johan Enell

Message:

Fixes #40

Location:

trunk/se/lu/onk/ZTest/src/ztest

Files:

• Plot.java (modified) (1 diff)
• Reporter.java (modified) (2 diffs)
• Spot.java (modified) (1 diff)
• Start.java (modified) (6 diffs)

trunk/se/lu/onk/ZTest/src/ztest/Plot.java

@@ -187 +187 @@
     throws IOException
   {
+    if (m.getItemCount(0) == 0)
+    {
+      System.err.println("Can't print histogram. Dataset empty.");
+      return;
+    }
+    
     NumberAxis domainAxis = new NumberAxis("M, log2(int1/int2)");
     NumberAxis rangeAxis1 = new NumberAxis("Frequence");

trunk/se/lu/onk/ZTest/src/ztest/Reporter.java

@@ -29 +29 @@
   private String reporter;
   private double m;
+  private double a;
   private double p;
   private int size;
   private String symbol;
   private String locusLink;
+  private int id;
   
   
-  public Reporter(String reporter, String symbol, String locusLink)
+  public Reporter(int id, String reporter, String symbol, String locusLink, double a)
   {
+    this.id = id;
     this.reporter = reporter;
     this.symbol = symbol;
     this.locusLink = locusLink;
+    this.a = a;
   }
 
@@ -60 +64 @@
   {
     return m;
+  }
+  
+  public double getA()
+  {
+    return a;
+  }
+  
+  public int getId()
+  {
+    return id;
   }
 

trunk/se/lu/onk/ZTest/src/ztest/Spot.java

@@ -26 +26 @@
 public class Spot
 {
-  double m;
+  private double m;
   
   public Spot(Double m)

trunk/se/lu/onk/ZTest/src/ztest/Start.java

@@ -59 +59 @@
 
       int mCol = assayFields.indexOf("l2ratio1_2");
+      int aCol = assayFields.indexOf("l10intgmean1_2");
       int repCol = columns.indexOf("reporter");
       int repidCol = columns.indexOf("reporterId");
@@ -65 +66 @@
       int assayDataCol = columns.indexOf("assayData");
 
-      if (mCol == -1 || repCol == -1 || repidCol == -1 || symCol == -1 || llCol == -1 || assayDataCol == -1)
+      if (aCol == -1 || mCol == -1 || repCol == -1 || repidCol == -1 || symCol == -1 || llCol == -1 || assayDataCol == -1)
       {
         throw new BASEFileException("Cant find the columns l2ratio1_2, reporter or assayData");
       }
       mCol += assayDataCol;
+      aCol += assayDataCol;
 
       int dataLength = columns.size() + assays.size() * assayFields.size() - 1;
-      bfss.setDataMatrix(bfss.findIntOpt("count"), assays.size() * assayFields.size());
+      bfss.setDataMatrix(bfss.findIntOpt("count"), assays.size());
       String[] data = bfr.readDataRow(dataLength);
       while (data != null)
       {
         Spot[] spots = new Spot[assays.size()];
+        Double a = 0.0;
+        int aCount = 0;
         for (int i = 0; i < assays.size(); i++)
         {
-          int index = mCol + i * assayFields.size();
+          int mIndex = mCol + i * assayFields.size();
+          int aIndex = aCol + i * assayFields.size();
           Double m = Double.NaN;
-          if (!data[index].equals(""))
+          if (!data[mIndex].equals(""))
+            m = new Double(data[mIndex]);
+          if (!data[aIndex].equals(""))
           {
-            m = new Double(data[index]);
+            a += new Double(data[aIndex]);
+            aCount++;
           }
           spots[i] = new Spot(m);
         }
-        Reporter r = new Reporter(data[repidCol], data[symCol], data[llCol]);
+        Reporter r = new Reporter(new Integer(data[repCol]), data[repidCol], data[symCol], data[llCol], a/aCount);
         bfss.addData(r, spots);
         data = bfr.readDataRow(dataLength);
@@ -140 +148 @@
       Object[] tableRow = {"Reporter","GeneSymbol","LocusLink","AverageM","up/down","P","Rank","Expected","FDR","NumberOfValues"};
 
+      System.out.println("BASEfile");
+      System.out.println("section\tassays");
+      System.out.println("annotationColumns\t");
+      System.out.println("columns\tid\tname\tparents");
+      System.out.println("count\t1");
+      System.out.println("%");
+      System.out.println("1\tztest\t"+bfss.findStringOpt("assays").replaceAll("\t", "/"));
+      System.out.println();
+      System.out.println("section\tspots");
+      System.out.println("channels\t2");
+      System.out.println("setExtraFloats\tJE_nbrOfElements\tJE_rank\tJE_Expected\tJE_fdr");
+      System.out.println("assayFields\tl2ratio1_2\tl10intgmean1_2\tJE_nbrOfElements\tJE_rank\tJE_Expected\tJE_fdr");
+      System.out.println("columns\tposition\treporter\tassayData");
+      System.out.println("assays\t1");
+      System.out.println("count\t"+bfss.getReporterSize());
+      System.out.println("%");
+      
       html.println("<!DOCTYPE html PUBLIC \"-//W3C//DTD XHTML 1.0 Frameset//EN\" \"http://www.w3.org/TR/xhtml1/DTD/xhtml1-frameset.dtd\">");
       html.println("<html>");
@@ -149 +174 @@
       html.println("<table>");
       html.printf("<tr><th>%s</th><th>%s</th><th>%s</th><th>%s</th><th>%s</th><th>%s</th><th>%s</th><th>%s</th><th>%s</th><th>%s</th></tr>\n", tableRow);
+      
       tab.printf("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n", tableRow);
 
@@ -158 +184 @@
         double fdr = (expected / rank);
         
+        System.out.printf("%d\t%d\t", (-1*rank), r.getId());
+        System.out.printf("%f\t%f\t", r.getM(), r.getA());
+        System.out.printf("%d\t%d\t%f\t%f\n", r.getSize(), rank, expected, fdr);
+        
+        tableRow[0] = r.getReporter();
+        tableRow[1] = r.getSymbol();
+        tableRow[2] = r.getLocusLink();
+        tableRow[3] = r.getM();
+        tableRow[4] = r.getM() > 0 ? "+" : "-";
+        tableRow[5] = r.getP();
+        tableRow[6] = rank;
+        tableRow[7] = expected;
+        tableRow[8] = fdr;
+        tableRow[9] = r.getSize();
+
         if (i < 1000)
         {
-          tableRow[0] = r.getReporter();
-          tableRow[1] = r.getSymbol();
-          tableRow[2] = r.getLocusLink();
-          tableRow[3] = r.getM();
-          tableRow[4] = r.getM() > 0 ? "+" : "-";
-          tableRow[5] = r.getP();
-          tableRow[6] = rank;
-          tableRow[7] = expected;
-          tableRow[8] = fdr;
-          tableRow[9] = r.getSize();
-          
           html.printf(
             "<tr class=\"row" + (i % 2 + 1) + "\"><td>%s</td><td>%s</td><td>%s</td><td>%f</td>" +
@@ -183 +213 @@
         mHist.addObservation(r.getM());
       }
+      System.out.println();
+      
       html.println("</table>");
       html.print("</html>");